Truls,
That looks to me like a crash where the PyMOL API was somehow
called before PyMOL was initialized...how and why this could happen is a
mystery to me though -- that's what pymol.finish_launching() is supposed
to prevent -- but there may be some flaw in the logic.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-Original Message-
From: Debian Chooser [mailto:ker...@herocamp.org] On Behalf Of Truls
A.
Tangstad
Sent: Friday, October 17, 2003 3:18 PM
To: Warren L. DeLano
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Using PyMol as a library - no GUI
On Fri, Oct 17, 2003 at 09:41:24AM -0700, Warren L. DeLano wrote:
Truls A. Tangstad wrote:
I'm very interested in using alot of the functionality that PyMol
offers programmatically from Python, i.e. without using a GUI at
all. The chempy package seems to cover alot of my needs, loading
different file formats etc. even though it doesn't seem to be
documented.
Is it also possible to use the rest of the functionality in PyMol
from
other Python scripts? Right now, just importing the pymol package
seems to force the GUI to open.
If you've got PyMOL configured to open on
import pymol
pymol.finish_launching()
You can suppress the GUI feature and suppress startup output by
providing command line arguments as follows. Before importing
PyMOL,
set a pymol_argv list in the __main__ namespace. PyMOL will
interpret
this as a sys.argv styled list of command line arguments.
import __main__
__main__.pymol_argv['pymol','-qc']
import pymol
pymol.finish_launching()
Thanks, seems to work like a charm in scripts after adding the
assignment operator:
__main__.pymol_argv = ['pymol', '-qc'] # adding miss
Somehow it segfaults when trying the same thing in an interactive
python interpreter though, right after importing pymol. This might be
due to a shoddy install on my part, but I'm including a gdb backtrace:
#0 0x41d7b21a in SettingGetGlobal_f () from /usr/lib/python2.3/site-
packages/pymol/_cmd.so
#1 0x41d7c683 in SettingGet () from /usr/lib/python2.3/site-
packages/pymol/_cmd.so
#2 0x41d6296d in OrthoAddOutput () from /usr/lib/python2.3/site-
packages/pymol/_cmd.so
#3 0x41d679a5 in PCatchInit () from /usr/lib/python2.3/site-
packages/pymol/_cmd.so
#4 0x4006d74d in PyCFunction_Call () from
/usr/lib/libpython2.3.so.1.0
#5 0x40045e37 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0
#6 0x400a2a4a in PyEval_CallObjectWithKeywords () from
/usr/lib/libpython2.3.so.1.0
#7 0x4000 in PyFile_WriteObject () from
/usr/lib/libpython2.3.so.1.0
#8 0x400556e6 in PyFile_WriteString () from
/usr/lib/libpython2.3.so.1.0
#9 0x400d56b6 in PySys_WriteStderr () from
/usr/lib/libpython2.3.so.1.0
#10 0x400d4b2c in PySys_WriteStderr () from
/usr/lib/libpython2.3.so.1.0
#11 0x400d2c74 in Py_AtExit () from /usr/lib/libpython2.3.so.1.0
#12 0x40101043 in _PyUnicode_TypeRecords () from
/usr/lib/libpython2.3.so.1.0
Any idea why it shouldn't work interactively?
I'm using PyMol 0.90 and Python 2.3.2 on Debian unstable.
--
Truls - kerfue+pymol-us...@herocamp.org
